Although I know some people cannot stand the inclusion of the Bat Family in the cinematic version of Batman. I think WB could literally have an ensemble project with Gotham City alone.

If you keep continuity with the Dark Knight trilogy, John "Robin" Blake is a problem with this concept, but you could always have him change his name to Tim Drake considering Tim's new origin in the comics. It even rhymes.
Since going "superhero" he has Bruce wipe him from records ala Selina Kyle
Have him just become Red Robin in the cinematic universe.

Anyway, The new film should take place a few years later in a much differnt Gotham. Bruce Wayne had come back to Gotham, claiming that he was locked away during the occupation by Bane.

The story would give us a much older, wiser, and more Detective style Batman. Sure he still kicks ass, but he uses his wits more.
Plus, he has a lot more assistance these days. Over the years he took in Dick Grayson who became Robin, and then graduated to Nightwing.

Gordons daughter Barbara even became Batgirl.

All told through a quick cut flashback sequence.

I do believe Arkham Asylum (both the GN and the Game) is the way to go for the reboot.
The nuts take over the nut house, and Batman has to go in. Him, and him alone.

His team handles things outside the asylum as gang wars escalate since they know Batman is occupied.
Penguin is at war with Black Mask over territory, etc.

Inside he would face, for the first time on film, a complete ensemble of Bat Villains.
Joker, Scarecrow, Riddler, Mad Hatter, Ivy, etc.

Inside he would unexpectedly gain assistance from a young guy named Jason Todd.

Jason would wind up beaten to a bloody pulp in the end by Joker, and assumed dead, Batman would leave him behind to finish his battle.

In the end, Batman would prevail, but end credits would see Jason still alive, and very upset with Batman for leaving him behind.

Then, instead of a direct sequel

Make The Red Hood a film.

Give all of Batman's now established allies there own film, building them up.

You could also give Batman solo films where the team is just cameos.

But the next time you bring them all together would be huge!

Sort of similar to the X-Men formula going on right now.
But imagine taking Wolverine now, and putting him in Avengers, it would be quite huge.

Batman's world fits this formula quite nicely.

People love seeing his villains all together, and his allies. A major threat to Gotham could handle the team ups.